How to run simulations with non-canonical amino acids?

for a current iGEM competition research project, we are considering using ROSETTA for protein structure predictions. However, as we have very limited experience with the software, we do not know how to start the computation.
For our project, we aim at evolving the Methanocaldococcus jannaschii tRNA-synthetase for the non-canonical amino acid nitrophenylalanine, and would like to simulate the process before doing it in practice. We were wondering whether there are any further information available online with regards to the simulation processes (e.g. protocols, helpful guides) for our purposes, or if anyone has done something similar and could provide us with protocols or scripts.

If I understand correctly, you are remodeling an existing enzyme to act on different substrate. The fact that your substrate happens to be a noncanonical amino acid is mostly irrelevant - what you're doing is enzyme specificity redesign.

We ran the enzyme design demo, which worked fine, but when trying to adapt the demo to our own tRNA-synthetasis/ncAA, we get the following error "The native pose does not have jump number 1". Are we missing any specific options or preprocessing steps for the PDB files?

So jumps are nonchemical kinematic connections between parts of your Pose. Rosetta functions on internal coordinates, not 3-D coordinates; thus all atoms must be connected by a kinematic framework of (pseudo-) bonds, angles, and torsions. Jumps are the nonchemical connections. There is at least one jump for every separate chemical entity - every chain, in PDB speak. Broadly, there is a jump for each thing not connected by a covalent bond.

"The native pose does not have jump number 1" implies that something in your system is expected to have a jump and does not. My best guess is that whatever it's interpreting as the "native pose" (are you doing RMSD calculations?) is missing its ligand. With no ligand, there is no jump to the ligand, which is probably the complaint.